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Easy Pumpkin Cheesecake Muffins with Cream Cheese Swirl

These Easy Pumpkin Cheesecake Muffins with Cream Cheese Swirl are one of those simple fall recipes that disappear quickly around our house. Pumpkin muffins are already soft and moist, but adding a swirl of sweet cream cheese makes them feel a little extra special without any extra fuss.

I like making a batch ahead for those busy autumn mornings when everyone is rushing out the door and a quick breakfast is all there is time for. They are also perfect tucked into lunchboxes, packed along for hockey practice, or enjoyed quietly with a hot cup of coffee on a cool fall afternoon.

Pumpkin cheesecake muffins with cream cheese swirl arranged on a white plate.

What you’ll love the Pumpkin Cheesecake Muffins


  • Cheesecake Swirl – A creamy swirl of sweetened cream cheese makes these muffins feel extra special.
  • Make Ahead – Bake a batch on the weekend for quick breakfasts and snacks throughout the week
  • Lunchbox Friendly – Easy to pack into lunchboxes, sports bags, or take along on busy days.
  • Soft and Moist – Pumpkin puree keeps the muffins tender and delicious for several days.
  • Freezer Friendly – Freeze a batch and thaw as needed for an easy fall treat.

How to Make Pumpkin Cheesecake Muffins

Ingredients for Pumpkin Cheesecake Muffins

Pumpkin Muffin Batter

  • 1 3/4 cups all-purpose flour
  • 2 teaspoons pumpkin pie spice
  • 1 teaspoon baking soda
  • 1/2 teaspoon salt
  • 15 ounces pumpkin puree
  • 1 cup granulated sugar
  • 1/2 cup brown sugar
  • 2 large eggs
  • 1/2 cup vegetable oil
  • 2 teaspoons vanilla extract

Cheesecake Swirl

  • 8 ounces cream cheese, softened
  • 1/4 cup granulated sugar
  • 1 large egg yolk
  • 1 teaspoon vanilla extract
Ingredients needed to make pumpkin cheesecake muffins with cream cheese swirl.

How to Make Pumpkin Cheesecake Muffins

Step 1: Prepare the Muffin Pan

Preheat the oven to 375°F and line 18 muffin cups with paper liners.

Step 2: Mix the Pumpkin Batter

In a large mixing bowl, whisk together the pumpkin puree, granulated sugar, brown sugar, eggs, vegetable oil, and 2 teaspoons vanilla extract until smooth.

Wet ingredients whisked together in a mixing bowl for pumpkin cheesecake muffins.

In a separate bowl, whisk together the flour, pumpkin pie spice, baking soda, and salt.

Dry ingredients whisked together in a large mixing bowl for pumpkin cheesecake muffins.

Add the dry ingredients to the pumpkin mixture and stir just until combined. Be careful not to overmix.

Pumpkin muffin batter mixed until smooth in a glass mixing bowl.

Step 3: Make the Cheesecake Swirl

In a medium bowl, beat the softened cream cheese and sugar until smooth and creamy. Add the egg yolk and the remaining teaspoon of vanilla extract and mix until well combined.

Cream cheese filling mixed until smooth for pumpkin cheesecake muffins.

Step 4: Fill and Swirl the Muffins

Fill each muffin liner about two-thirds full with pumpkin batter. Add about 1 tablespoon of the cream cheese mixture to the center of each muffin.

A muffin baking tray will with pumpkin batter and cheesecake filling thats been swirled.

Use a toothpick or skewer to gently swirl the cream cheese into the tops of the muffins.

Step 5: Bake and Cool

Bake for 18 to 20 minutes, or until a toothpick inserted into the pumpkin portion of a muffin comes out clean.

Let the muffins cool in the pan for 5 minutes before transferring them to a wire rack to cool completely.

Pumpkin cheesecake muffins with cream cheese swirl arranged on a white plate.

Storage and Freezing

Store leftover pumpkin cheesecake muffins in an airtight container in the refrigerator for up to 5 days. Because of the cream cheese swirl, they should be refrigerated once completely cooled.

To freeze, place the cooled muffins in a freezer-safe container or bag and freeze for up to 3 months. Thaw overnight in the refrigerator or at room temperature before serving.

Pumpkin cheesecake muffin with a bite removed showing the moist pumpkin crumb.

Pin It For Later

If you’re as excited about pumpkin season as I am, be sure to save these Easy Pumpkin Cheesecake Muffins with Cream Cheese Swirl for later. They’re a delicious make-ahead treat for busy fall mornings, lunchboxes, and cozy afternoons with a cup of coffee.

A stack of pumpkin cheesecake muffins with a cream cheese swirl.  The Pinterest graphic states pumpkin cheesecake muffin with cream cheese swirl.

Easy pumpkin cheesecake muffins with cream cheese swirl on a white plate.

Easy Pumpkin Cheesecake Muffins with Cream Cheese Swirl

These pumpkin cheesecake muffins are soft, moist, and full of warm fall flavor. A creamy cheesecake swirl makes them extra special and perfect for breakfast, snacks, or lunchboxes.
Prep Time 15 minutes
Cook Time 18 minutes
Total Time 33 minutes

Ingredients
  

Pumpkin Muffin Batter

  • cups all-purpose flour
  • 2 teaspoons pumpkin pie spice
  • 1 teaspoon baking soda
  • ½ teaspoon salt
  • 15 ounces pumpkin puree
  • 1 cup granulated sugar
  • ½ cup brown sugar
  • 2 large eggs
  • ½ cup vegetable oil
  • 2 teaspoons vanilla extract

Cheesecake Swirl

  • 8 ounces cream cheese softened
  • ¼ cup granulated sugar

Instructions
 

  • Preheat oven to 375°F and line 18 muffin cups with paper liners.
  • In a large bowl, whisk together the pumpkin puree, granulated sugar, brown sugar, eggs, vegetable oil, and 2 teaspoons vanilla extract until smooth.
  • In a separate bowl, whisk together the flour, pumpkin pie spice, baking soda, and salt.
  • Add the dry ingredients to the pumpkin mixture and stir just until combined.
  • In a medium bowl, beat the cream cheese and ¼ cup granulated sugar until smooth.
  • Add the egg yolk and remaining teaspoon vanilla extract and mix until combined.
  • Fill each muffin liner about two-thirds full with pumpkin batter.
  • Add about 1 tablespoon of cream cheese mixture to the center of each muffin.
  • Use a toothpick or skewer to gently swirl the cream cheese mixture into the tops of the muffins.
  • Bake for 18 to 20 minutes, or until a toothpick inserted into the pumpkin portion of a muffin comes out clean.
  • Cool in the pan for 5 minutes before transferring to a wire rack to cool completely.

Notes

  • Use pure pumpkin puree, not pumpkin pie filling.
  • Allow the cream cheese to soften before mixing for the smoothest cheesecake swirl.
  • Stir the batter just until combined. Overmixing can result in dense muffins.
  • The exact yield will vary depending on the size of your muffin pan and how full you fill the liners. This recipe makes approximately 12 large bakery-style muffins or up to 18 standard-sized muffins.
  • Because of the cream cheese swirl, store leftover muffins in the refrigerator once completely cooled.
  • Freeze cooled muffins in an airtight container for up to 3 months. Thaw in the refrigerator or at room temperature before serving.

More Pumpkin Recipe to Try

Like many people, I love all things pumpkin spice. It’s my favorite baking season, even more so than fresh berry season, which is hard to believe, I know. I have plenty of pumpkin recipes I could share, but I’ve narrowed it down to these three favorites.

Pumpkin bread recipe bakes and being served as a thick slice. You an see a coffee cup in the background, and the pumpkin bread has a layer of sout cream on glaze on it.

Pumpkin Bread with Sour Cream and Glaze

This moist pumpkin bread is one of my favorite fall baking recipes. Made with sour cream and warm pumpkin spice, it has a tender crumb and a sweet glaze that makes it perfect for breakfast, snacking, or sharing with friends and family.

A single serving of pumpkin mousse with a swirl of whipped cream and a sprinkle of cinnamon sugar. The pumpkin dessert is served with a gingersnap stuffed into the whipped cream and another gingersnap cookie placed on the side of the serving plate.

Pumpkin Mousse with Brown Sugar Whipped Cream

This easy pumpkin mousse is light, creamy, and full of warm fall flavor. Topped with homemade brown sugar whipped cream, it’s a simple make-ahead dessert that’s both fancyy enoughfor Thanksgiving, holiday gatherings, or anytime you’re craving a pumpkin treat.

A small white bowl filled with four separate piles of spices. There is cinnamon, nutmeg, ginger and allspice.

Homemade Pumpkin Pie Spice

When a recipe calls for pumpkin pie spice and you discover you’re out, this simple homemade blend comes together in minutes using common pantry spices.

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